Details:

Personal Author:
Mwenda, Mulenga ; Saasa, Ngonda ; Sinyange, Nyambe ; Busby, George ; Chipimo, Peter J. ; ... More +
Mwenda, Mulenga ; Saasa, Ngonda ; Sinyange, Nyambe ; Busby, George ; Chipimo, Peter J. ; Hendry, Jason ; Kapona, Otridah ; Yingst, Samuel ; Hines, Jonas Z. ; Minchella, Peter ; Simulundu, Edgar ; Changula, Katendi ; Nalubamba, King Shimumbo ; Sawa, Hirofumi ; Kajihara, Masahiro ; Yamagishi, Junya ; Kapin’a, Muzala ; Kapata, Nathan ; Fwoloshi, Sombo ; Zulu, Paul ; Mulenga, Lloyd B. ; Agolory, Simon ; Mukonka, Victor ; Bridges, Daniel J. Less -
Corporate Authors:
PATH (Lusaka, Zambia) ; University of Zambia. School of Veterinary Medicine. ; Zambia National Public Health Institute. ; Wellcome Trust Centre for Human Genetics (Oxford, England) ; CDC Zambia. ; ... More +
PATH (Lusaka, Zambia) ; University of Zambia. School of Veterinary Medicine. ; Zambia National Public Health Institute. ; Wellcome Trust Centre for Human Genetics (Oxford, England) ; CDC Zambia. ; Hokkaido University (Research Center for Zoonosis Control) ; Zambia. Ministry of Health. Less -
Description:
The first laboratory-confirmed cases of coronavirus disease 2019 (COVID-19), the illness caused by SARS-CoV-2, in Zambia were detected in March 2020 (1). Beginning in July, the number of confirmed cases began to increase rapidly, first peaking during July–August, and then declining in September and October (Figure). After 3 months of relatively low case counts, COVID-19 cases began rapidly rising throughout the country in mid-December. On December 18, 2020, South Africa published the genome of a SARS-CoV-2 variant strain with several mutations that affect the spike protein (2). The variant included a mutation (N501Y) associated with increased transmissibility.†,§ SARS-CoV-2 lineages with this mutation have rapidly expanded geographically.¶,** The variant strain (PANGO [Phylogenetic Assignment of Named Global Outbreak] lineage B.1.351††) was first detected in the Eastern Cape Province of South Africa from specimens collected in early August, spread within South Africa, and appears to have displaced the majority of other SARS-CoV-2 lineages circulating in that country (2). As of January 10, 2021, eight countries had reported cases with the B.1.351 variant. In Zambia, the average number of daily confirmed COVID-19 cases increased 16-fold, from 44 cases during December 1–10 to 700 during January 1–10, after detection of the B.1.351 variant in specimens collected during December 16–23. Zambia is a southern African country that shares substantial commerce and tourism linkages with South Africa, which might have contributed to the transmission of the B.1.351 variant between the two countries.

Since September 2020, University of Zambia and PATH (https://www.path.orgexternal icon) have routinely been conducting genetic epidemiologic studies using whole genome sequencing (WGS) on SARS-CoV-2–positive specimens. A subset of specimens collected during March 18–December 23, 2020, were sequenced, from which 268 high-quality genomes were generated. Specimens were selected for WGS based on availability and real-time reverse transcription–polymerase chain reaction (RT-PCR) diagnostic test cycle threshold (Ct) values of <30; lower Ct values are correlated with larger amounts of virus in the sample. Sequences were linked to case investigation information including patient age, sex, and geographic location from routine public health data maintained by the Zambia National Public Health Institute. For WGS, complementary DNA was prepared using random primers from viral RNA extracted from SARS-CoV-2 real-time RT-PCR–positive specimens. Multiplex PCR was then performed using custom primers (3) to generate overlapping amplicons for nanopore sequencing on a MinION (Oxford Nanopore Technology, United Kingdom).§§ Consensus sequence reads were generated using the standard ARTIC Network bioinformatic pipeline,¶¶ a system for processing samples from viral disease outbreaks to generate real-time, actionable epidemiologic information.

Suggested citation for this article: Mwenda M, Saasa N, Sinyange N, et al. Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020. MMWR Morb Mortal Wkly Rep. ePub: 17 February 2021.

mm7008e2.htm?s_cid=mm7008e2_w

mm7008e2-H.pdf


Subject:
[+]
Clinical Laboratory Techniques Contact Tracing Coronavirus Infections/diagnosis COVID-19 Testing Mutation SARS-CoV-2/genetics
Series:
MMWR. Morbidity and mortality weekly report ; v. 70, early release, February 17, 2021
Document Type:
Journal Article
Place as Subject:
Zambia
Collection(s):
Morbidity and Mortality Weekly Report (MMWR)
Main Document Checksum:
[+]
urn:sha256:65898c8fb7cef2a79727ff97fbe39a135a06cbc366d41bb6227f9357d67f4a66
Download URL:
https://stacks.cdc.gov/view/cdc/102801/cdc_102801_DS1.pdf
File Type:

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